Photosensitive behaviors and circadian rhythms are well documented in reef-building corals and their larvae, yet photoreceptive structures and opsins have not been described in these organisms. Here I provide evidence for red sensitivity in several species of coral larvae. Behavioral experiments with two Caribbean corals, Porites astreoides and Acropora palmata demonstrated that larvae settle and metamorphose at a greater frequency on red substrata than on similar substrata of other colors. Attachment to red substrata was not observed when larvae were maintained in the dark, suggesting that red sensitivity was responsible for the observed behavior. Extracellular recordings confirm photosensitivity and indicate that the peak sensitivity of coral photoreceptors are shifted towards the orange-red region of the visible light spectrum, similar to the spectra (fluorescence and reflectance) of preferred artificial (plastic) and natural (crustose coralline algae) settlement substrata. Using Blast analyses and a PCRbased approach, I have identified, sequenced and cloned two full-length opsin cDNAs from A. palmata larvae. One cDNA (Acropsin 1) encodes an opsin protein that is similar to a vertebrate melanopsin; the second (Acropsin 2) encodes a protein that is most similar to cephalopod rod opsin. I have successfully developed synthetic peptide antibodies against each Acropsin 1 and Acropsin 2. Western blots of adult A. palmata and A. cervicornis protein detect a 37kDa and 40kDa band, corresponding to the predicted molecular weights of Acropsins 1 and 2, respectively. Immunohistochemistry confirms expression of both opsins in A. palmata larvae. Staining of sectioned larvae demonstrates that Acropsin 1 is localized in the larval gastroderm while Acropsin 2 is localized in solitary epithelial cells, scattered throughout the larval ectoderm but with a polarized distribution and higher concentration in the aboral epidermis. This research provides several lines of evidence to support the existence, and demonstrate one potential ecological function, of opsin-based photosensitivity in corals.

Les espèces coralliennes Acropora palmata (Lamarck, 1816) et A. cervicornis (Lamarck, 1816) ont un rôle majeur en termes de bio-construction et structuration des récifs dans la Caraïbe. Cependant, les populations de ces deux espèces sont en déclin et elles sont maintenant classées en danger critique d’extinction par l’Union Internationale de Conservation de la Nature (UICN). De récentes études principalement menées sur les récifs de la Floride et des Grandes Antilles se sont ainsi intéressé à la structure et à la dynamique des populations de ces espèces, mais le statut génétique des populations des Petites Antilles est moins connu.Le présent sujet a pour but d’étudier l’état des populations des coraux Acropora palmata et A. cervicornis sur les récifs de Guadeloupe et des Petites Antilles et d’élucider les mécanismes qui président à la survie de ces espèces et au recrutement des jeunes coraux. / In the Caribbean, Acropora palmata (Lamarck 1816) and A. cervicornis (Lamarck 1816) are major coral species for reef building. Since the 80’s, these species populations are decreasing and are now classified as critically endangered species by the International Union for Conservation of Nature (IUCN). Recent studies, mainly conducted on the reefs of Florida and the Greater Antilles concerned the structure and the dynamics of Acropora populations, while the genetic status of the populations in the Lesser Antilles remains less studied. The purpose of the study is to determine the status of the coral populations of Acropora palmata and A. cervicornis on reefs of Guadeloupe and Lesser Antilles and to elucidate the mechanisms governing the survival of these species and the recruitment of young corals.

This thesis is composed of two articles. The first is an analysis of long-term survival among A. cervicornis outplants in the Florida Keys, from 2007 to the present. The second is a review of literature that informs coral restoration and guides both restoration practitioners and coral researchers towards greater effectiveness in outplant survival and understanding biological processes involved in restoration. In the first article, despite promising initial evidence of outplant survival and health, the long-term results, using Weibull survival analysis, are discouraging with almost all out planted corals over an 8 year long study exhibiting steep declines in percent live tissue and survival between three and five years. Not only is this 3-5 year collapse apparent in all the outplanted cohorts, but the evidence is highly significant that the length of outplant survival is decreasing with each passing year (diminished resilience). These findings suggest that some shared, likely environmental factor, is increasingly impacting all outplants. Further, no cohorts appear to adapt to the environmental conditions in which these declines are occurring (diminished adaptive capacity), a trend that would be evident if their declines slowed or reversed and Weibull beta-parameterization would show. The second article, reviews several areas of recent study which offer avenues for future research: these include, ecological history and biogeography, developmental pathways of colonial form and function, polarity and symmetry, genetics, wound healing, fecundity, reproduction, sexual maturity and community interactions. The thesis concludes with questions for further research and understanding in the field of coral restoration.

While populations of nearly all stony coral species along the Florida reef tract have exhibited decline, the most notable decline has occurred in the once-dominant acroporid species (Acropora cervicornis, A. palmata). Both species were listed in 2006 as threatened under the Endangered Species Act. This listing, combined with their continued decline, has resulted in large-scale restoration efforts throughout Florida and the Western Caribbean. Currently, there is little to no information regarding spatial prioritization of sites for these restoration efforts. The primary objective of this dissertation was to utilize species distribution modeling, informed by existing data from the Florida reef tract, to identify sites for restoration of acroporid corals that should have strong likelihood for success. The initial focus was to use a database of reported field observations, in combination with benthic habitat maps, to model the extent of suitable habitat for Acropora spp. The mapped coral reef and hardbottom classifications throughout Florida, Puerto Rico, and the US Virgin Island reef tracts were used to generate potential-habitat polygons using buffers that incorporated 95% and 99% of reported observations of Acropora spp. Resulting maps demonstrated that A. palmata habitat is relatively well defined, while that of A. cervicornis is more variable and difficult to constrain. Thus, as the major focus of this dissertation, available monitoring data from the Florida reef tract were used to construct and compare two types of statistical species distribution models, random forest and boosted classification trees, as an approach to inform siting of restoration efforts for A. cervicornis. Boosted classification trees were more accurate than the random forest model at classifying A. cervicornis population trends. Further analyses of the two most important environmental parameters identified by the model, depth and light availability, revealed that reef areas predicted to not have had A. cervicornis present from 1996-2013 were deeper, on average, and had lower light availability and greater variance than areas predicted to have had continuous or transient A. cervicornis presence over this time frame. This study represents a first step at deriving an ecologically-guided approach to spatial prioritization of restoration efforts. The overarching goal of this project has been to design a strategy for creating models to define and predict where conservation and restoration actions should be most effective, that can be utilized for a variety of coral species. With existing populations mapped, the results can also aid in protecting the limited areas in which these species still occur.

Since the 1980’s, there has been an unprecedented decline in the reef-building Caribbean corals, Acropora cervicornis and A. palmata, which has led to their listing as “threatened” under the U.S Endangered Species Act. Despite this protective status, these Acropora species continue to experience declines primarily attributed to disease, global climate change, and storm damage. Recent evidence suggests the hybrid of these threatened species (A. prolifera) is found at abundances similar to or higher than the parental species at many sites throughout the Caribbean. However, there is still much that is unknown as to how and why hybrids may be increasing in abundance at select sites. In 2007, scientists from NOAA NMFS established 9 permanent transects at three sites in the USVI to quantify fish diversity and coral tissue condition in A. cervicornis thickets. Over the years, they observed that A. prolifera seemed to be increasing in abundance on transects that were once dominated by A. cervicornis. This dataset provided a unique opportunity to investigate whether a shift from a threatened parental species to its hybrid may have occurred. This study has two objectives, (1) to quantify the change in A. cervicornis and A. prolifera percent cover and colony health over a 9-year period, and (2) to compare the genotypic diversity among the three Caribbean acroporids on and near the transects to determine the primary method of propagation, i.e., sexual versus asexual. For this study, I used transect photographs taken in March, July and November 2009, April 2012, and August 2017 to compare intra- and interannual variation in acroporid cover and colony health. Striking losses were observed in A. cervicornis cover between March 2009 and August 2017. At Thatch Cay, A. cervicornis declined from 25.7% to 8.9% between March 2009 and November 2009, but remained stable (10.2%) up to August 2017. Acropora cervicornis cover declined from 13.2% to 0% at Lovango Cay, and from 8.2% to 0% at No-Name Bay. At the one site (No-Name Bay) that A. prolifera was present during the original surveys of the transects, the percent cover remained relatively high and stable over the sample period. At No-Name Bay, A. prolifera percent cover (18.2%) was significantly higher than A. cervicornis (5.4%) by November 2009. It appears that A. prolifera expanded in the habitat left void by the decline in A. cervicornis. The general health of A. cervicornis based on the amount of healthy versus white and pale tissue appeared to decline at all sites between March 2009 and November 2009. To determine if the high percent cover on some transects was derived from asexual propagation or sexual recruitment, 139 tissue samples were collected in 2017 and genotyped using five microsatellite markers. No significant difference in genotypic richness (number of unique genotypes divided by the sample size) was observed among A. cervicornis (0.62), A. prolifera (0.64), and A. palmata (0.68). This suggests that the hybrid colonization is from multiple sexually derived individuals, not just asexual propagation from a rare hybridization event. High genotypic diversity, stable population abundance, and healthier colonies, suggest acroporid hybrids may become the primary habitat building coral of shallow reefs in the U.S. Virgin Islands. Due to considerable differences in morphologies between A. cervicornis and A. prolifera, it is unclear how a shift to the hybrid may affect the organisms that occupy acroporid structure and if the same ecological functions can be fulfilled.

Elkhorn and Staghorn corals (Acropora palmata, A. cervicornis) were listed as threatened species under the Endangered Species Act (ESA) in 2005. The threatened status of these species is unprecedented given the vital role they historically played as major constructors of western Atlantic and Caribbean coral reefs. The goal of my study was to evaluate the current extent of habitat of the two species using a database of reported in situ observations. From these observations, potential habitat maps were produced based on benthic substrata and depth parameters throughout the Florida reef tract using GIS software. Locations of 99% of A. palmata observations and 84% of A. cervicornis observations coincided with previously mapped reef or hardbottom habitat. These results indicate that potential habitat for A. palmata is currently well defined and that potential habitat for A. cervicornis is more variable than that for A. palmata. This study provides a starting point in the creation of a revised critical habitat delineation for Acropora spp. in Florida. Using the mapped reef and hardbottom classifications throughout the Florida reef tract, probable habitat maps were generated using buffers that incorporated 95% and 99% of reported observations of colonies of Acropora spp. One of the most important differences between the previously generated critical habitat map and the new probable habitat map is observed in the southeast Florida region, where probable habitat extends further north than critical habitat and, thus, encompasses additional habitat for A. cervicornis and potentially A. palmata.

The reefs off Broward County exist as three shore-parallel, sequentially deeper terraces named the "inner", "middle", and "outer" reefs and also a shallower, nearshore ridge complex. These structures span the continental coast of southeast Florida from Palm Beach County to southern Miami-Dade County and were characterized as relict, early Holocene shelf-edge and mid-shelf reefs along with limestone ridges. Presently, the reefs are colonized by a fauna characteristic of West Atlantic/Caribbean reef systems. Scleractinian coral cover is low except for a few dense patches of Acropora cervicornis, while Acropora palmata is absent except for a few individual living colonies. Coral reef core-drilling is a useful analytical tool to extract observable and datable geological samples from within reefs. This technique was employed to retrieve 4 cores from the inner reef off Broward County to better understand its age, composition, and Holocene growth history. Sub-samples from corals in cores provided 7 new radiocarbon ages ranging from 7,860-5,560 cal BP, and reef accumulation rates of l.7-2.45 m/1,000 yrs were calculated from these ages. In addition, coral species composition and taphonomic characteristics were analyzed to identify former reef environments/reef zonation, and signals for inner reef termination. Reef zonation was detectable but no clear taphonomic signal for inner reef termination was evident. Current data and radiocarbon ages from all three Broward County reefs suggest that the outer reef accumulated from ~10.6-8 ka cal BP, the middle reef from at least ~5.8-3.7 ka cal BP, and the inner reef from ~7.8-5.5 ka cal BP. A lack of significant age overlaps between the three reefs has led to the assertion that they represent backstepping reefs in response to Holocene sea-level rise. This study has provided the oldest and youngest ages from the inner reef thus far, and confirms that reef backstepping from the outer reef to the inner reef occurred within just a few hundred years after the termination of the outer reef. The middle reef remains poorly understood and thus a definitive Holocene growth history and ultimately an understanding of their formation are still largely unknown.